Free Energy Analysis of a Conformational Change of Heme ABC Transporter BhuUV-T

The heme ATP-binding cassette (ABC) transporter BhuUV-T of bacterial pathogen Burkholderia cenocepacia is required to transport heme across the inner cell membrane. The current hypothesis is that the binding of two ATPs to the nucleotide-binding domains of the transporter drives the initial steps of the transport cycle in which the empty transport sites are reoriented from the cytosol to the periplasm. Molecular details are missing because the structure of a key occluded intermediate remains hypothetical. Here we perform molecular simulations to analyze the free energy surface (FES) of the first step of the reorientation, namely the transition from an open inward-facing (IF) transport site to an occluded (Occ) conformation. We have modeled the latter structure in silico in a previous study. A simple annealing procedure removes residual bias originating from non-equilibrium targeted molecular dynamics. The calculated FES reveals the role of the ATPs in inducing the IF → Occ conformational change and validates the modeled Occ conformation.